Apple didn't collude with Amazon.
Publishers may or may not have colluded with each other.
Apple simply offered publishers a deal that they liked better than the one Amazon was offering. This is how competition is supposed to work. They liked the deal so much that they may have put pressure on each other to go along with it, and pressure on Amazon to renegotiate the deal they had with Amazon. But, somehow, somebody got it in their head that Apple did something wrong.
Basically if anyone did anything wrong, it's the publishers. But they settled, so we'll never really know. Meanwhile Apple gets caught up in the middle of it, when the net result of their actions was to create greater competition in the marketplace, and the breaking up of Amazon's monopoly.